Hidden breakpoints in genome alignments

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7534 LNBI, Issue , 2012, Pages 391-403

  Kehr, Birte ^a,b   Reinert, Knut ^a   Darling, Aaron E ^c  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNERS; BREAK-POINTS; BREAKPOINT; EVOLUTIONARY DISTANCE; GENOME ALIGNMENT; LARGE-SCALE STRUCTURE; LOWER BOUNDS; MEDIAN PROBLEM; PAIR-WISE COMPARISON; RELATIVE RATES; SIMULATED DATASETS; TIME COMPLEXITY;

ALIGNMENT; BIOINFORMATICS; BIOLOGY; EVOLUTIONARY ALGORITHMS;

GENES;

EID: 84866639055     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-33122-0_31     Document Type: Conference Paper

References (16)

1. Angiuoli, S.V., Salzberg, S.L.: Mugsy: fast multiple alignment of closely related whole genomes. Bioinformatics 27(3), 334-342 (2011)
2. Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F.A., Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., Haussler, D., Miller, W.: Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res. 14(4), 708-715 (2004)
3. Darling, A.C.E., Mau, B., Blattner, F.R., Perna, N.T.: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14(7), 1394-1403 (2004)
4. Darling, A.E., Mau, B., Perna, N.T.: progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5(6), 11147 (2010)
5. De, S., Michor, F.: DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes. Nat. Biotechnol. 29(12), 1103-1108 (2011)
6. Delcher, A.L., Phillippy, A., Carlton, J., Salzberg, S.L.: Fast algorithms for largescale genome alignment and comparison. Nucleic Acids Res. 30(11), 2478-2483 (2002)
7. Fudenberg, G., Getz, G., Meyerson, M., Mirny, L.A.: High order chromatin architecture shapes the landscape of chromosomal alterations in cancer. Nat. Biotechnol. 29(12), 1109-1113 (2011)
8. Greenman, C.D., Pleasance, E.D., Newman, S., Yang, F., Fu, B., Nik-Zainal, S., Jones, D., Lau, K.W., Carter, N., Edwards, P.A.W., Futreal, P.A., Stratton, M.R., Campbell, P.J.: Estimation of rearrangement phylogeny for cancer genomes. Genome Res. 22(2), 346-361 (2012)
9. Kolmogorov, V.: Blossom V: a new implementation of a minimum cost perfect matching algorithm. Mathematical Programming Computation 1, 43-67 (2009)
10. Medini, D., Donati, C., Tettelin, H., Masignani, V., Rappuoli, R.: The microbial pan-genome. Curr. Opin. Genet. Dev. 15(6), 589-594 (2005)
11. Nowacki, M., Shetty, K., Landweber, L.F.: RNA-mediated epigenetic programming of genome rearrangements. Annu. Rev. Genomics Hum. Genet. 12, 367-389 (2011)
12. Rambaut, A., Grassly, N.C.: Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13(3), 235-238 (1997)
13. Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.C., Haussler, D., Miller, W.: Human-mouse alignments with BLASTZ. Genome Res. 13(1), 103-107 (2003)
14. Tannier, E., Zheng, C., Sankoff, D.: Multichromosomal median and halving problems under different genomic distances. BMC Bioinformatics 10, 120 (2009)
15. Umbarger, M.A., Toro, E., Wright, M.A., Porreca, G.J., Ba, D., Hong, S.H., Fero, M.J., Zhu, L.J., Marti-Renom, M.A., McAdams, H.H., Shapiro, L., Dekker, J., Church, G.M.: The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol. Cell. 44(2), 252-264 (2011)
16. Zhang, Y., Hu, F., Tang, J.: Phylogenetic reconstruction with gene rearrangements and gene losses. In: Park, T., Tsui, S.K.W., Chen, L., Ng, M.K., Wong, L., Hu, X. (eds.) BIBM, pp. 35-38. IEEE Computer Society (2010)